ec0445a92ee03d852427a766d78df32b78140aa6
mspeir
Tue Apr 15 10:04:41 2014 -0700
Adding entries for balAcu1 release, refs #12977
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<font size="4"><a name="TOC"></a><b> News</b></font><a href="http://www.twitter.com/GenomeBrowser" target="_blank"><img src="http://twitter-badges.s3.amazonaws.com/t_small-a.png" alt="Follow GenomeBrowser on Twitter" style="vertical-align:text-bottom; margin-left: 15px;"></a></TD>
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<P>
To receive announcements of new genome
assembly releases, new software features, updates and
training seminars by email, subscribe to the
<A HREF="http://groups.google.com/a/soe.ucsc.edu/group/genome-announce?hl=en"
TARGET=_blank>genome-announce</A> mailing list.</P>
<!-- start news -->
<hr>
<p>
+ <font face="courier" size="3"><b>15 April 2014 -
+ New Minke Whale (balAcu1) Assembly Now Available in the Genome Browser</b></font>
+ <p>
+ A Genome Browser is now available for the minke whale (Balaenoptera acutorostrata scammoni)
+ assembly released October 2013 by the <A HREF="http://eng.kiost.ac/kordi_eng/main/" TARGET="_BLANK">
+ Korea Ocean Research & Development Institute</A> (KORDI version BalAcu1.0, UCSC version balAcu1).
+ For more information and statistics about this assembly, see the NCBI assembly record for
+ <A HREF="http://www.ncbi.nlm.nih.gov/assembly/78761" TARGET="_BLANK">BalAcu1.0</A>. There are
+ 10,776 scaffolds with a total size of 2,431,687,698 bases.
+ </p>
+
+ <p>
+ Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
+ <A HREF="ftp://hgdownload.cse.ucsc.edu/goldenPath/balAcu1/">FTP server</A> or the
+ <A HREF="http://hgdownload.cse.ucsc.edu/downloads.html#minke_whale">Downloads</A> page. Please
+ observe the <A HREF="goldenPath/credits.html#minke_whale_use">conditions for use</A> when accessing and
+ using these data sets. The annotation tracks for this browser were generated by UCSC and
+ collaborators worldwide. See the <A HREF="goldenPath/credits.html#minke_whale_credits">Credits</A>
+ page for a detailed list of the organizations and individuals who contributed to this release.
+ </p>
+
+ <hr>
+ <p>
<font face="courier" size="3"><b>11 April 2014 -
New UCSC Genes Track Released for GRCm38/mm10</b></font>
<p>
We're happy to announce the release of an updated UCSC Genes track for the GRCm38/mm10
mouse Genome Browser. The new release has 61,642 total transcripts, compared with 59,121
in the previous version. The total number of canonical genes has increased from 31,469
to 32,408. Comparing the new gene set with the previous version:
<ul>
<li>54,714 transcripts did not change between versions.</li>
<li>19 transcripts were not carried forward to the new version.</li>
<li>3,866 transcripts are "compatible" with those in the previous set, meaning
that the two transcripts show consistent splicing. In most cases, the old and new
transcripts differ in the lengths of their UTRs.</li>
<li>522 transcripts overlap with those in the previous set, but do not show consistent
splicing (i.e., they contain overlapping introns with differing splice sites).</li>
</ul>
</p>
<p>
More details about the new UCSC Genes track can be found on the
<a href="../cgi-bin/hgTrackUi?db=mm10&g=knownGene">UCSC Genes track
description page</a>.
</p>
+ <hr>
- <p>
- Many thanks to Brian Raney and Steve Heitner for their work on this track!
- </p>
+ <!-- staged for archive use
- <hr>
- <p>
- <font face="courier" size="3"><b>06 March 2014 -
- The new GRCh38 Human Genome Browser is here!</b></font>
- <p>
- In the final days of 2013, the
- <a href="http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/"
- target="_blank">Genome Reference Consortium</a> (GRC) released the eagerly awaited GRCh38
- human genome assembly, the first major revision of the human genome in more than four
- years. During the past two months, the UCSC team has been
- hard at work building a browser that will let our users explore the new
- assembly using their favorite Genome Browser features and tools.
- Today we're announcing the release of a preliminary browser on the GRCh38
- assembly. Although we still have plenty of work ahead of us in constructing the rich
- feature set that our users have come to expect, this early release will allow you to
- take a peek at what's new.
- <p>
- Starting with this release, the UCSC Genome Browser version numbers for human
- assemblies will match those of the GRC to minimize version confusion. Hence, the GRCh38
- assembly is referred to as hg38 in Genome Browser datasets and documentation. We've
- also made some slight changes to our chromosome naming scheme that affect primarily the
- names of haplotype chromosomes, unplaced contigs and unlocalized contigs. For more details
- about this, see the
- <a href="../cgi-bin/hgGateway?db=hg38">hg38 gateway page</a>.
<p>
- <b>What's new in GRCh38?</b>
- <ul>
- <li>
- <b>Alternate sequences</b> - Several human chromosomal regions exhibit sufficient
- variability to prevent adequate representation by a single sequence. To address this, the
- GRCh38 assembly provides alternate sequence for selected variant regions through the
- inclusion of <em>alternate loci scaffolds</em> (or <em>alt loci</em>). Alt loci are
- separate accessioned sequences that are aligned to reference chromosomes. This assembly
- contains 261 alt loci, many of which are associated with the LRC/KIR area of chr19 and the
- MHC region on chr6. (See the
- <a href="../cgi-bin/hgTracks?chromInfoPage=">sequences</a> page for a complete list of the
- reference chromosomes and alternate sequences in GRCh38.)
- <li>
- <b>Centromere representation</b> - Debuting in this release, the large megabase-sized gaps
- that were previously used to represent centromeric regions in human assemblies have been
- replaced by sequences from centromere models created by
- <a href="http://genome.cshlp.org/content/24/4/697.abstract"
- target="_blank">Karen Miga et al.</a>, using centromere databases developed during her
- work in the <a href="http://www.genome.duke.edu/labs/WillardLab/"
- target="_blank">Willard lab</a> at
- Duke University and analysis software developed while working in the
- <a href="http://cbse.soe.ucsc.edu/people/kent" target="_blank">Kent lab</a> at UCSC.
- The models, which provide the
- approximate repeat number and order for each centromere, will be useful for read mapping
- and variation studies.
- <li>
- <b>Mitochondrial genome</b> - The mitochondrial reference sequence included in the GRCh38
- assembly and hg38 Genome Browser (termed "chrM" in the browser) is the
- <a href="http://mitomap.org/bin/view.pl/MITOMAP/HumanMitoSeq"
- target="_blank">Revised Cambridge Reference Sequence</a> (rCRS) from
- <a href="http://mitomap.org/MITOMAP" target="_blank">MITOMAP</a> with GenBank accession
- number J01415.2 and RefSeq accession number NC_012920.1. This differs from the chrM
- sequence (RefSeq accession number NC_001907) used by the previous hg19 Genome Browser,
- which was not updated when the GRCh37 assembly later transitioned to the new version.
- <li>
- <b>Sequence updates</b> - Several erroneous bases and misassembled regions in GRCh37 have
- been corrected in the GRCh38 assembly, and more than 100 gaps have been filled or reduced.
- Much of the data used to improve the reference sequence was obtained from other genome
- sequencing and analysis projects, such as the <a href="http://www.1000genomes.org/"
- target="_blank">1000 Genomes Project</a>.
- <li>
- <b>Analysis set</b> - The GRCh38 assembly offers an "analysis set" that was
- created to accommodate next generation sequencing read alignment pipelines. Several
- GRCh38 regions have been eliminated from this set to improve read mapping.
- The analysis set may be downloaded from the Genome Browser
- <a href="http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/"
- target="_blank">downloads page</a>.
- </ul>
- <p>
- For more information about the files included in the GRCh38 GenBank submission,
- see the
- <a href="ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/README"
- target="_blank">GRCh38 README</a>. The GRCh38 GenBank record provides a detailed
- array of <a href="http://www.ncbi.nlm.nih.gov/assembly/883148/#/st_Primary-Assembly"
- target="_blank">statistics about this assembly</a>.
- Bulk downloads of the sequence and annotation data may be obtained from the Genome
- Browser <a href="ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/">FTP server</a>
- or the
- <a href="http://hgdownload.cse.ucsc.edu/downloads.html#human">Downloads</a>
- page. The annotation tracks for this browser were generated by UCSC and collaborators
- worldwide.
- </p>
- <p>
- <b>Much more to come!</b> This initial release of the hg38 Genome Browser provides a
- rudimentary set of annotations. Many of our annotations rely on data sets from external
- contributors (such as our popular SNPs tracks) or require massive computational effort
- (our comparative genomics tracks). In the upcoming months/years, we will release many more
- annotation tracks as they become available. To stay abreast of new datasets, join our
- <a href="http://groups.google.com/a/soe.ucsc.edu/group/genome-announce?hl=en"
- target="_blank">genome-announce</a> mailing list or follow us on
- <a href="http://www.twitter.com/GenomeBrowser" target="_blank">twitter</a>.
+ <font face="courier" size="3"><b>15 April 2014 -
+ New Minke Whale (balAcu1) Assembly Now Available in the
+ Genome Browser</b></font>
+ A Genome Browser is now available for the minke whale
+ (Balaenoptera acutorostrata scammoni) assembly released
+ October 2013 by the Korea Ocean Research & Development Institute.
+ <a href="goldenPath/newsarch.html#041514">Read more</a>.
</p>
- We'd like to thank our GRC and NCBI collaborators who worked closely with
- us in producing the hg38 browser. Their quick responses and helpful feedback were a
- key factor in expediting this release. The production of the hg38 Genome Browser was
- a team effort, but in particular we'd like to acknowledge the engineering efforts of Hiram
- Clawson and Brian Raney, the QA work done by Steve Heitner, project guidance
- provided by Ann Zweig, Robert Kuhn, and Jim Kent, and documentation work by Donna
- Karolchik.
- See the <a href="goldenPath/credits.html#human_credits">Credits</a> page for a detailed
- list of the organizations and individuals who contributed to this release.
- </p>
- <p>
- <hr>
-
- <!-- staged for archive use
<p>
<font face="courier" size="3"><b>11 April 2014 -
New UCSC Genes Track Released for GRCm38/mm10</b></font>
</p>
We're happy to announce the release of an updated UCSC Genes
track for the GRCm38/mm10 mouse Genome Browser.
<a href="goldenPath/newsarch.html#041114">Read more</a>.
</p>
+ -->
+ <!-- start archives -->
<p>
<font face="courier" size="3"><b>06 March 2014 -
The new GRCh38 Human Genome Browser is here!</b></font>
- </p>
In the final days of 2013, the Genome Reference Consortium (GRC)
released the eagerly awaited GRCh38 human genome assembly, the
first major revision of the human genome in more than four years.
<a href="goldenPath/newsarch.html#030614">Read more</a>.
</p>
- -->
- <!-- start archives -->
-
<p>
<font face="courier" size="3"><b>04 March 2014 -
Introducing Genome Browser highlight feature:</b></font>
We are excited to announce a new highlight feature in the UCSC
Genome Browser. Using drag-and-select, you can now highlight a
region or gene of interest.
<a href="goldenPath/newsarch.html#030414">Read more</a>.
</p>
- <font face="courier" size="3"><b>28 February 2014 -
- New! Expanded onsite workshop program!:</b></font>
- Explore the full power of the UCSC Genome Browser!
- Thanks to the funding support of NHGRI, we can now offer hands-on Genome Browser
- training onsite at your institution.
- <a href="goldenPath/newsarch.html#022814">Read more</a>.
- </p>
-
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